# Source code for MDAnalysis.coordinates.DMS

    # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
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    # R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
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    # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
    # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
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    """
    DESRES file format --- :mod:`MDAnalysis.coordinates.DMS`
    ========================================================

    Classes to read DESRES_ Molecular Structure file format (DMS_)
    coordinate files (as used by the Desmond_ MD package).

    .. _DESRES: http://www.deshawresearch.com
    .. _Desmond: http://www.deshawresearch.com/resources_desmond.html
    .. _DMS: http://www.deshawresearch.com/Desmond_Users_Guide-0.7.pdf
    """
    import numpy as np
    import sqlite3

    from . import base
    from .core import triclinic_box

    class DMSReader(base.SingleFrameReaderBase):
        """
        Reads both coordinates and velocities.

        .. versionchanged:: 0.11.0
           Frames now 0-based instead of 1-based
        """

        format = "DMS"
        units = {"time": None, "length": "A", "velocity": "A/ps"}

        def get_coordinates(self, cur):
            cur.execute("SELECT * FROM particle")
            particles = cur.fetchall()
            return [(p["x"], p["y"], p["z"]) for p in particles]

        def get_particle_by_columns(self, cur, columns=None):
            if columns is None:
                columns = ["x", "y", "z"]
            cur.execute("SELECT * FROM particle")
            particles = cur.fetchall()
            return [tuple([p[c] for c in columns]) for p in particles]

        def get_global_cell(self, cur):
            cur.execute("SELECT * FROM global_cell")
            rows = cur.fetchall()
            assert len(rows) == 3
            x = [row["x"] for row in rows]
            y = [row["y"] for row in rows]
            z = [row["z"] for row in rows]
            return {"x": x, "y": y, "z": z}

        def _read_first_frame(self):
            coords_list = None
            velocities_list = None

            def dict_factory(cursor, row):
                d = {}
                for idx, col in enumerate(cursor.description):
                    d[col[0]] = row[idx]
                return d

            with sqlite3.connect(self.filename) as con:
                # This will return dictionaries instead of tuples, when calling cur.fetch() or fetchall()
                con.row_factory = dict_factory
                cur = con.cursor()
                coords_list = self.get_coordinates(cur)
                velocities_list = self.get_particle_by_columns(
                    cur, columns=["vx", "vy", "vz"]
                )
                unitcell = self.get_global_cell(cur)

            if not coords_list:
                raise IOError("Found no coordinates")
            self.n_atoms = len(coords_list)

            velocities = np.array(velocities_list, dtype=np.float32)
            if not velocities.any():
                velocities = None

            self.ts = self._Timestep.from_coordinates(
                np.array(coords_list, dtype=np.float32),
                velocities=velocities,
                **self._ts_kwargs,
            )
            self.ts.frame = 0  # 0-based frame number

            self.ts.dimensions = triclinic_box(
                unitcell["x"], unitcell["y"], unitcell["z"]
            )

            if self.convert_units:
                self.convert_pos_from_native(self.ts._pos)  # in-place !
                if self.ts.dimensions is not None:
                    self.convert_pos_from_native(
                        self.ts.dimensions[:3]
                    )  # in-place !
                if self.ts.has_velocities:
                    # converts nm/ps to A/ps units
                    self.convert_velocities_from_native(self.ts._velocities)